Running questions

  • Below are some questions to revisit during further analysis
    • Should we look at data from last decade only rather than last 30 years?
    • How to structure this document
      • climate variable (MAT, MAP)
        • compare across symptoms (filtered?)
        • compare across ‘number of unhealthy trees’
        • compare across size class?
        • compare across site type?

Data Prep

Import data

Data downloaded manually from iNat.

Prepare dataset for extracting environmental data with climateNA

30 Normals

Import dataset with 30yr normals data

Merge data

Clean data

Add consistency to factors

Symptoms
##  [1] "Branch Dieback or 'Flagging'"                      
##  [2] "Browning Canopy"                                   
##  [3] "Extra Cone Crop"                                   
##  [4] "Healthy"                                           
##  [5] "Multiple Symptoms (please list in Notes)"          
##  [6] "New Dead Top (red or brown needles still attached)"
##  [7] "Old Dead Top (needles already gone)"               
##  [8] "Other (please describe in Notes)"                  
##  [9] "Thinning Canopy"                                   
## [10] "Tree is dead"                                      
## [11] "Yellowing Canopy"
Unhealthy trees
## [1] "0"            "1"            "2-3"          "4-6"          "7-10"        
## [6] "More than 10" "Not sure"
Tree size
## [1] ""                                                             
## [2] "Large (too big to wrap arms around trunk)"                    
## [3] "Medium (can wrap arms around trunk)"                          
## [4] "No selection"                                                 
## [5] "Other"                                                        
## [6] "Small (can wrap hands around trunk)"                          
## [7] "Very Large (would take many people to wrap arms around trunk)"

Filter data

Only include symptoms of interest

## [1] "Healthy"                                           
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"               
## [4] "Thinning Canopy"                                   
## [5] "Tree is dead"

Data Exploration

MAT

Symptoms

Site Severity
Size Class

MAP

Symptoms

AHM

Symptoms

SHM

Symptoms

Filtered SHM <200

MSP

Symptoms

CMD

Symptoms

Eref

Symptoms

Decade 2011-2020

Import dataset with Decade 2011-2020

Merge data

Clean data

Add consistency to factors

Symptoms
##  [1] "Branch Dieback or 'Flagging'"                      
##  [2] "Browning Canopy"                                   
##  [3] "Extra Cone Crop"                                   
##  [4] "Healthy"                                           
##  [5] "Multiple Symptoms (please list in Notes)"          
##  [6] "New Dead Top (red or brown needles still attached)"
##  [7] "Old Dead Top (needles already gone)"               
##  [8] "Other (please describe in Notes)"                  
##  [9] "Thinning Canopy"                                   
## [10] "Tree is dead"                                      
## [11] "Yellowing Canopy"
Unhealthy trees
## [1] "0"            "1"            "2-3"          "4-6"          "7-10"        
## [6] "More than 10" "Not sure"
Tree size
## [1] ""                                                             
## [2] "Large (too big to wrap arms around trunk)"                    
## [3] "Medium (can wrap arms around trunk)"                          
## [4] "No selection"                                                 
## [5] "Other"                                                        
## [6] "Small (can wrap hands around trunk)"                          
## [7] "Very Large (would take many people to wrap arms around trunk)"

Filter data

Only include symptoms of interest

## [1] "Healthy"                                           
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"               
## [4] "Thinning Canopy"                                   
## [5] "Tree is dead"

Data Exploration

MAT

Symptoms

Site Severity
Size Class

MAP

Symptoms

AHM

Symptoms

SHM

Symptoms

Filtered SHM <200

MSP

Symptoms

CMD

Symptoms

Eref

Symptoms

Large Trees on Severe sites

MSP

Symptoms

CMD

Symptoms

TOPO Data

Import TOPO Data

Merge data

Clean data

Add consistency to factors

Symptoms
##  [1] "Branch Dieback or 'Flagging'"                      
##  [2] "Browning Canopy"                                   
##  [3] "Extra Cone Crop"                                   
##  [4] "Healthy"                                           
##  [5] "Multiple Symptoms (please list in Notes)"          
##  [6] "New Dead Top (red or brown needles still attached)"
##  [7] "Old Dead Top (needles already gone)"               
##  [8] "Other (please describe in Notes)"                  
##  [9] "Thinning Canopy"                                   
## [10] "Tree is dead"                                      
## [11] "Yellowing Canopy"
Unhealthy trees
## [1] "0"            "1"            "2-3"          "4-6"          "7-10"        
## [6] "More than 10" "Not sure"
Tree size
## [1] ""                                                             
## [2] "Large (too big to wrap arms around trunk)"                    
## [3] "Medium (can wrap arms around trunk)"                          
## [4] "No selection"                                                 
## [5] "Other"                                                        
## [6] "Small (can wrap hands around trunk)"                          
## [7] "Very Large (would take many people to wrap arms around trunk)"

Filter data

Only include symptoms of interest

## [1] "Healthy"                                           
## [2] "New Dead Top (red or brown needles still attached)"
## [3] "Old Dead Top (needles already gone)"               
## [4] "Thinning Canopy"                                   
## [5] "Tree is dead"

Data Exploration

Aspect

Symptoms
##   [1] "id"                                                                                     
##   [2] "observed_on_string"                                                                     
##   [3] "observed_on"                                                                            
##   [4] "time_observed_at"                                                                       
##   [5] "time_zone"                                                                              
##   [6] "user_id"                                                                                
##   [7] "user_login"                                                                             
##   [8] "created_at"                                                                             
##   [9] "updated_at"                                                                             
##  [10] "quality_grade"                                                                          
##  [11] "license"                                                                                
##  [12] "url"                                                                                    
##  [13] "image_url"                                                                              
##  [14] "sound_url"                                                                              
##  [15] "tag_list"                                                                               
##  [16] "description"                                                                            
##  [17] "num_identification_agreements"                                                          
##  [18] "num_identification_disagreements"                                                       
##  [19] "captive_cultivated"                                                                     
##  [20] "oauth_application_id"                                                                   
##  [21] "place_guess"                                                                            
##  [22] "latitude"                                                                               
##  [23] "longitude"                                                                              
##  [24] "positional_accuracy"                                                                    
##  [25] "private_place_guess"                                                                    
##  [26] "private_latitude"                                                                       
##  [27] "private_longitude"                                                                      
##  [28] "public_positional_accuracy"                                                             
##  [29] "geoprivacy"                                                                             
##  [30] "taxon_geoprivacy"                                                                       
##  [31] "coordinates_obscured"                                                                   
##  [32] "positioning_method"                                                                     
##  [33] "positioning_device"                                                                     
##  [34] "place_town_name"                                                                        
##  [35] "place_county_name"                                                                      
##  [36] "place_state_name"                                                                       
##  [37] "place_country_name"                                                                     
##  [38] "place_admin1_name"                                                                      
##  [39] "place_admin2_name"                                                                      
##  [40] "species_guess"                                                                          
##  [41] "scientific_name"                                                                        
##  [42] "common_name"                                                                            
##  [43] "iconic_taxon_name"                                                                      
##  [44] "taxon_id"                                                                               
##  [45] "field.tree.canopy.symptoms"                                                             
##  [46] "field.optional...did.the.tree.have.heat.damage"                                         
##  [47] "field.percent.canopy.affected...."                                                      
##  [48] "field.number.of.additional.unhealthy.trees..of.same.species..in.area..within.sight."    
##  [49] "field.percent.of.trees..of.same.species..within.sight.that.are.unhealthy"               
##  [50] "field.other.factors...are.there.signs.or.symptoms.of.insect..diseases..or.other.damage."
##  [51] "field.optional...what..other.factors..were.observed."                                   
##  [52] "field.optional...tree.size"                                                             
##  [53] "field.optional...site.type"                                                             
##  [54] "field.optional...site.location.description"                                             
##  [55] "field.optional...site.area.disturbance.level"                                           
##  [56] "field.optional...site.hydrology"                                                        
##  [57] "field.optional...access.to.water"                                                       
##  [58] "field.optional...slope.position"                                                        
##  [59] "field.optional...were.there.any.other.unhealthy.plant.species.on.the.site."             
##  [60] "field.optional...timing.of.symptoms.estimate"                                           
##  [61] "field.optional...estimated.time.spent.to.make.this.observation....of.minutes."          
##  [62] "field.optional...can.we.follow.up.with.you."                                            
##  [63] "field.notes"                                                                            
##  [64] "X"                                                                                      
##  [65] "Latitude"                                                                               
##  [66] "Longitude"                                                                              
##  [67] "Elevation"                                                                              
##  [68] "Tmax01"                                                                                 
##  [69] "Tmax02"                                                                                 
##  [70] "Tmax03"                                                                                 
##  [71] "Tmax04"                                                                                 
##  [72] "Tmax05"                                                                                 
##  [73] "Tmax06"                                                                                 
##  [74] "Tmax07"                                                                                 
##  [75] "Tmax08"                                                                                 
##  [76] "Tmax09"                                                                                 
##  [77] "Tmax10"                                                                                 
##  [78] "Tmax11"                                                                                 
##  [79] "Tmax12"                                                                                 
##  [80] "Tmin01"                                                                                 
##  [81] "Tmin02"                                                                                 
##  [82] "Tmin03"                                                                                 
##  [83] "Tmin04"                                                                                 
##  [84] "Tmin05"                                                                                 
##  [85] "Tmin06"                                                                                 
##  [86] "Tmin07"                                                                                 
##  [87] "Tmin08"                                                                                 
##  [88] "Tmin09"                                                                                 
##  [89] "Tmin10"                                                                                 
##  [90] "Tmin11"                                                                                 
##  [91] "Tmin12"                                                                                 
##  [92] "Tave01"                                                                                 
##  [93] "Tave02"                                                                                 
##  [94] "Tave03"                                                                                 
##  [95] "Tave04"                                                                                 
##  [96] "Tave05"                                                                                 
##  [97] "Tave06"                                                                                 
##  [98] "Tave07"                                                                                 
##  [99] "Tave08"                                                                                 
## [100] "Tave09"                                                                                 
## [101] "Tave10"                                                                                 
## [102] "Tave11"                                                                                 
## [103] "Tave12"                                                                                 
## [104] "PPT01"                                                                                  
## [105] "PPT02"                                                                                  
## [106] "PPT03"                                                                                  
## [107] "PPT04"                                                                                  
## [108] "PPT05"                                                                                  
## [109] "PPT06"                                                                                  
## [110] "PPT07"                                                                                  
## [111] "PPT08"                                                                                  
## [112] "PPT09"                                                                                  
## [113] "PPT10"                                                                                  
## [114] "PPT11"                                                                                  
## [115] "PPT12"                                                                                  
## [116] "Rad01"                                                                                  
## [117] "Rad02"                                                                                  
## [118] "Rad03"                                                                                  
## [119] "Rad04"                                                                                  
## [120] "Rad05"                                                                                  
## [121] "Rad06"                                                                                  
## [122] "Rad07"                                                                                  
## [123] "Rad08"                                                                                  
## [124] "Rad09"                                                                                  
## [125] "Rad10"                                                                                  
## [126] "Rad11"                                                                                  
## [127] "Rad12"                                                                                  
## [128] "DD_0_01"                                                                                
## [129] "DD_0_02"                                                                                
## [130] "DD_0_03"                                                                                
## [131] "DD_0_04"                                                                                
## [132] "DD_0_05"                                                                                
## [133] "DD_0_06"                                                                                
## [134] "DD_0_07"                                                                                
## [135] "DD_0_08"                                                                                
## [136] "DD_0_09"                                                                                
## [137] "DD_0_10"                                                                                
## [138] "DD_0_11"                                                                                
## [139] "DD_0_12"                                                                                
## [140] "DD5_01"                                                                                 
## [141] "DD5_02"                                                                                 
## [142] "DD5_03"                                                                                 
## [143] "DD5_04"                                                                                 
## [144] "DD5_05"                                                                                 
## [145] "DD5_06"                                                                                 
## [146] "DD5_07"                                                                                 
## [147] "DD5_08"                                                                                 
## [148] "DD5_09"                                                                                 
## [149] "DD5_10"                                                                                 
## [150] "DD5_11"                                                                                 
## [151] "DD5_12"                                                                                 
## [152] "DD_18_01"                                                                               
## [153] "DD_18_02"                                                                               
## [154] "DD_18_03"                                                                               
## [155] "DD_18_04"                                                                               
## [156] "DD_18_05"                                                                               
## [157] "DD_18_06"                                                                               
## [158] "DD_18_07"                                                                               
## [159] "DD_18_08"                                                                               
## [160] "DD_18_09"                                                                               
## [161] "DD_18_10"                                                                               
## [162] "DD_18_11"                                                                               
## [163] "DD_18_12"                                                                               
## [164] "DD18_01"                                                                                
## [165] "DD18_02"                                                                                
## [166] "DD18_03"                                                                                
## [167] "DD18_04"                                                                                
## [168] "DD18_05"                                                                                
## [169] "DD18_06"                                                                                
## [170] "DD18_07"                                                                                
## [171] "DD18_08"                                                                                
## [172] "DD18_09"                                                                                
## [173] "DD18_10"                                                                                
## [174] "DD18_11"                                                                                
## [175] "DD18_12"                                                                                
## [176] "NFFD01"                                                                                 
## [177] "NFFD02"                                                                                 
## [178] "NFFD03"                                                                                 
## [179] "NFFD04"                                                                                 
## [180] "NFFD05"                                                                                 
## [181] "NFFD06"                                                                                 
## [182] "NFFD07"                                                                                 
## [183] "NFFD08"                                                                                 
## [184] "NFFD09"                                                                                 
## [185] "NFFD10"                                                                                 
## [186] "NFFD11"                                                                                 
## [187] "NFFD12"                                                                                 
## [188] "PAS01"                                                                                  
## [189] "PAS02"                                                                                  
## [190] "PAS03"                                                                                  
## [191] "PAS04"                                                                                  
## [192] "PAS05"                                                                                  
## [193] "PAS06"                                                                                  
## [194] "PAS07"                                                                                  
## [195] "PAS08"                                                                                  
## [196] "PAS09"                                                                                  
## [197] "PAS10"                                                                                  
## [198] "PAS11"                                                                                  
## [199] "PAS12"                                                                                  
## [200] "Eref01"                                                                                 
## [201] "Eref02"                                                                                 
## [202] "Eref03"                                                                                 
## [203] "Eref04"                                                                                 
## [204] "Eref05"                                                                                 
## [205] "Eref06"                                                                                 
## [206] "Eref07"                                                                                 
## [207] "Eref08"                                                                                 
## [208] "Eref09"                                                                                 
## [209] "Eref10"                                                                                 
## [210] "Eref11"                                                                                 
## [211] "Eref12"                                                                                 
## [212] "CMD01"                                                                                  
## [213] "CMD02"                                                                                  
## [214] "CMD03"                                                                                  
## [215] "CMD04"                                                                                  
## [216] "CMD05"                                                                                  
## [217] "CMD06"                                                                                  
## [218] "CMD07"                                                                                  
## [219] "CMD08"                                                                                  
## [220] "CMD09"                                                                                  
## [221] "CMD10"                                                                                  
## [222] "CMD11"                                                                                  
## [223] "CMD12"                                                                                  
## [224] "RH01"                                                                                   
## [225] "RH02"                                                                                   
## [226] "RH03"                                                                                   
## [227] "RH04"                                                                                   
## [228] "RH05"                                                                                   
## [229] "RH06"                                                                                   
## [230] "RH07"                                                                                   
## [231] "RH08"                                                                                   
## [232] "RH09"                                                                                   
## [233] "RH10"                                                                                   
## [234] "RH11"                                                                                   
## [235] "RH12"                                                                                   
## [236] "CMI01"                                                                                  
## [237] "CMI02"                                                                                  
## [238] "CMI03"                                                                                  
## [239] "CMI04"                                                                                  
## [240] "CMI05"                                                                                  
## [241] "CMI06"                                                                                  
## [242] "CMI07"                                                                                  
## [243] "CMI08"                                                                                  
## [244] "CMI09"                                                                                  
## [245] "CMI10"                                                                                  
## [246] "CMI11"                                                                                  
## [247] "CMI12"                                                                                  
## [248] "Tmax_wt"                                                                                
## [249] "Tmax_sp"                                                                                
## [250] "Tmax_sm"                                                                                
## [251] "Tmax_at"                                                                                
## [252] "Tmin_wt"                                                                                
## [253] "Tmin_sp"                                                                                
## [254] "Tmin_sm"                                                                                
## [255] "Tmin_at"                                                                                
## [256] "Tave_wt"                                                                                
## [257] "Tave_sp"                                                                                
## [258] "Tave_sm"                                                                                
## [259] "Tave_at"                                                                                
## [260] "PPT_wt"                                                                                 
## [261] "PPT_sp"                                                                                 
## [262] "PPT_sm"                                                                                 
## [263] "PPT_at"                                                                                 
## [264] "Rad_wt"                                                                                 
## [265] "Rad_sp"                                                                                 
## [266] "Rad_sm"                                                                                 
## [267] "Rad_at"                                                                                 
## [268] "DD_0_wt"                                                                                
## [269] "DD_0_sp"                                                                                
## [270] "DD_0_sm"                                                                                
## [271] "DD_0_at"                                                                                
## [272] "DD5_wt"                                                                                 
## [273] "DD5_sp"                                                                                 
## [274] "DD5_sm"                                                                                 
## [275] "DD5_at"                                                                                 
## [276] "DD_18_wt"                                                                               
## [277] "DD_18_sp"                                                                               
## [278] "DD_18_sm"                                                                               
## [279] "DD_18_at"                                                                               
## [280] "DD18_wt"                                                                                
## [281] "DD18_sp"                                                                                
## [282] "DD18_sm"                                                                                
## [283] "DD18_at"                                                                                
## [284] "NFFD_wt"                                                                                
## [285] "NFFD_sp"                                                                                
## [286] "NFFD_sm"                                                                                
## [287] "NFFD_at"                                                                                
## [288] "PAS_wt"                                                                                 
## [289] "PAS_sp"                                                                                 
## [290] "PAS_sm"                                                                                 
## [291] "PAS_at"                                                                                 
## [292] "Eref_wt"                                                                                
## [293] "Eref_sp"                                                                                
## [294] "Eref_sm"                                                                                
## [295] "Eref_at"                                                                                
## [296] "CMD_wt"                                                                                 
## [297] "CMD_sp"                                                                                 
## [298] "CMD_sm"                                                                                 
## [299] "CMD_at"                                                                                 
## [300] "RH_wt"                                                                                  
## [301] "RH_sp"                                                                                  
## [302] "RH_sm"                                                                                  
## [303] "RH_at"                                                                                  
## [304] "CMI_wt"                                                                                 
## [305] "CMI_sp"                                                                                 
## [306] "CMI_sm"                                                                                 
## [307] "CMI_at"                                                                                 
## [308] "MAT"                                                                                    
## [309] "MWMT"                                                                                   
## [310] "MCMT"                                                                                   
## [311] "TD"                                                                                     
## [312] "MAP"                                                                                    
## [313] "MSP"                                                                                    
## [314] "AHM"                                                                                    
## [315] "SHM"                                                                                    
## [316] "DD_0"                                                                                   
## [317] "DD5"                                                                                    
## [318] "DD_18"                                                                                  
## [319] "DD18"                                                                                   
## [320] "NFFD"                                                                                   
## [321] "bFFP"                                                                                   
## [322] "eFFP"                                                                                   
## [323] "FFP"                                                                                    
## [324] "PAS"                                                                                    
## [325] "EMT"                                                                                    
## [326] "EXT"                                                                                    
## [327] "MAR"                                                                                    
## [328] "Eref"                                                                                   
## [329] "CMD"                                                                                    
## [330] "RH"                                                                                     
## [331] "CMI"                                                                                    
## [332] "DD1040"
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).

Slope

Symptoms
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).

Elevation

Symptoms
## Warning: Removed 36 rows containing non-finite values (stat_boxplot).

Topo & Climate

Slope

CMD
## Warning: Removed 36 rows containing missing values (geom_point).

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 36 rows containing non-finite values (stat_smooth).

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 36 rows containing non-finite values (stat_smooth).

Elevation

##  [1] "field_1"     "id"          "lat"         "long"        "el"         
##  [6] "Aspect"      "Profilecurv" "Tangentialc" "Slope"       "PNWSRTMDEM"
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 36 rows containing non-finite values (stat_smooth).

Binary Data

## [1] "Healthy"   "Unhealthy"

Topo

## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 36 rows containing non-finite values (stat_smooth).

## Warning: Removed 36 rows containing non-finite values (stat_boxplot).

Climate

Data Exploration

MAT

Symptoms

Site Severity
Size Class

MAP

Symptoms

AHM

Symptoms

SHM

Symptoms

Filtered SHM <200

MSP

Symptoms

CMD

Symptoms

Eref

Symptoms

Large Trees on Severe sites

MSP

Symptoms

CMD

Symptoms